fix(vectorstore): walk and read the brain through brainfs (#157, slice 3) (#166)

vectorstore.Sync walks and reads via brainfs (regular files only, handle-checked), so symlinked notes are no longer embedded and their old chunks are purged. brainfs.WalkRegular requires every component of its root to be a real directory (fixes in-brain root aliasing in Sync and search Wing/Wing+Hall). Walk errors, including a symlinked scan root, abort Sync before the delete pass. brainfs gains Lstat. Directory-swap race recorded as accepted residual (#167).

Refs #157. Adversarial review: BLOCKED, BLOCKED, PASS.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Mathias <mthbqv@gmail.com>

ingestion/internal/api/readnote_root_test.go

@@ -0,0 +1,43 @@
+package api_test
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/api"
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs/brainfstest"
+)
+
+// hyperguild#157 slice 2: ReadNote (brain_get, read-after-write) read by
+// path; it now reads through brainfs.
+func TestReadNoteRefusesSymlinksAndSurvivesSwapRaces(t *testing.T) {
+	brain := t.TempDir()
+	facts := filepath.Join(brain, "wiki", "w", "facts")
+	require.NoError(t, os.MkdirAll(facts, 0o755))
+	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(facts, "leak.md")))
+	_, body, _, err := api.ReadNote(brain, "wiki/w/facts/leak.md")
+	assert.Error(t, err)
+	assert.NotContains(t, body, brainfstest.Sentinel)
+
+	p := filepath.Join(facts, "r.md")
+	require.NoError(t, os.WriteFile(p, []byte("---\nx: y\n---\ninside"), 0o644))
+	fm, body, _, err := api.ReadNote(brain, "wiki/w/facts/r.md")
+	require.NoError(t, err)
+	assert.Equal(t, "y", fm["x"])
+	assert.Contains(t, body, "inside")
+	read := func() string {
+		fm, body, _, _ := api.ReadNote(brain, "wiki/w/facts/r.md")
+		s := body
+		for k, v := range fm {
+			s += k + v
+		}
+		return s
+	}
+	brainfstest.AssertNoLeak(t, p, "---\nx: y\n---\ninside", 1500*time.Millisecond, read)
+	brainfstest.AssertNoHang(t, p, "---\nx: y\n---\ninside", 1500*time.Millisecond, 6*time.Second, func() { _ = read() })
+}

ingestion/internal/api/update.go

@@ -4,6 +4,7 @@ import (
 	"crypto/sha256"
 	"encoding/hex"
 	"fmt"
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 	"os"
 	"path/filepath"
 	"strings"
@@ -174,11 +175,17 @@ func UpdateNote(brainDir string, opts UpdateNoteOptions) (relPath, contentHash,
 // write primitive behind brain_get: the hash it returns equals the hash
 // brain_write / brain_update returned for the same bytes.
 func ReadNote(brainDir, relPath string) (fm map[string]string, body, contentHash string, err error) {
-	_, abs, err := resolveWithin(brainDir, relPath)
+	rel, _, err := resolveWithin(brainDir, relPath)
 	if err != nil {
 		return nil, "", "", err
 	}
-	raw, err := os.ReadFile(abs)
+	// Through the brain root, regular files only (hyperguild#157).
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return nil, "", "", fmt.Errorf("read note: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
+	raw, err := bfs.ReadRegular(rel)
 	if err != nil {
 		if os.IsNotExist(err) {
 			return nil, "", "", fmt.Errorf("note %q does not exist", relPath)

ingestion/internal/brainfs/brainfs.go

@@ -0,0 +1,201 @@
+// Package brainfs reads the brain directory through an os.Root (hyperguild#157).
+// The brain dir is a Syncthing sendreceive folder and Syncthing syncs
+// symlinks; a reader that walks and reads by path follows a planted symlink
+// out of the brain, and blocks forever on a planted FIFO. Readers that go
+// through a Brain only ever read regular files inside the brain: os.Root
+// refuses to leave the root even if an entry is swapped mid-read, and every
+// open is non-blocking with the type checked on the opened handle.
+package brainfs
+
+import (
+	"errors"
+	"fmt"
+	"io"
+	"io/fs"
+	"os"
+	"path"
+	"path/filepath"
+	"strings"
+	"syscall"
+)
+
+// ErrNotRegular is returned for an entry that is not a regular file.
+var ErrNotRegular = errors.New("not a regular file")
+
+// ErrTooLarge is returned by ReadRegularMax for a file over the limit.
+var ErrTooLarge = errors.New("file too large")
+
+// Brain is an open brain directory.
+type Brain struct {
+	root *os.Root
+	dir  string
+}
+
+// Open opens brainDir (which may itself be a mount symlink) as a root.
+func Open(brainDir string) (*Brain, error) {
+	r, err := os.OpenRoot(brainDir)
+	if err != nil {
+		return nil, fmt.Errorf("open brain root: %w", err)
+	}
+	return &Brain{root: r, dir: brainDir}, nil
+}
+
+// Close releases the root.
+func (b *Brain) Close() error { return b.root.Close() }
+
+// Rel converts a path under the brain dir to a root-relative path.
+func (b *Brain) Rel(path string) (string, error) {
+	rel, err := filepath.Rel(b.dir, path)
+	if err != nil {
+		return "", err
+	}
+	if rel == ".." || len(rel) > 2 && rel[:3] == ".."+string(filepath.Separator) {
+		return "", fmt.Errorf("%s is outside the brain dir", path)
+	}
+	return filepath.ToSlash(rel), nil
+}
+
+// Lstat stats a brain-relative path through the root without following a
+// final symlink.
+func (b *Brain) Lstat(rel string) (fs.FileInfo, error) {
+	return b.root.Lstat(filepath.ToSlash(rel))
+}
+
+// realDir returns ErrNotRegular unless every component of rel is a real
+// directory. A swap after the check is not caught (accepted residual,
+// hyperguild#157).
+func (b *Brain) realDir(rel string) error {
+	if rel == "." {
+		return nil
+	}
+	prefix := ""
+	for _, part := range strings.Split(rel, "/") {
+		prefix = path.Join(prefix, part)
+		fi, err := b.root.Lstat(prefix)
+		if err != nil {
+			return err
+		}
+		if !fi.IsDir() {
+			return fmt.Errorf("%s: walk root component %s is not a directory: %w", rel, prefix, ErrNotRegular)
+		}
+	}
+	return nil
+}
+
+// ReadRegular reads a brain-relative path, refusing anything that is not a
+// regular file, both before the open and on the opened handle.
+func (b *Brain) ReadRegular(rel string) ([]byte, error) {
+	fi, err := b.root.Lstat(rel)
+	if err != nil {
+		return nil, err
+	}
+	if !fi.Mode().IsRegular() {
+		return nil, fmt.Errorf("%s: %w", rel, ErrNotRegular)
+	}
+	return b.readOpened(rel)
+}
+
+// readOpened opens rel non-blocking and reads it only if the OPENED handle is
+// a regular file. This is the check that matters under a race: an entry
+// swapped for a FIFO after the Lstat, with a writer holding it open, would
+// otherwise park io.ReadAll forever (PR #161 review: removing it hung search
+// after 16 iterations).
+//
+// Accepted residual, as in api/rawroot.go: a HARD link to an outside file is
+// a regular file and is read. Syncthing syncs contents, not links, so a peer
+// cannot create one; fs.protected_hardlinks=1 and the pod's secrets are on a
+// different filesystem from the brain volume, so a local caller cannot link
+// them in. Refusing Nlink > 1 is the next step if either changes.
+func (b *Brain) readOpened(rel string) ([]byte, error) { return b.readOpenedMax(rel, -1) }
+
+// ReadRegularMax is ReadRegular with a size limit, checked on the opened
+// handle before reading (max < 0 means no limit).
+func (b *Brain) ReadRegularMax(rel string, max int64) ([]byte, error) {
+	fi, err := b.root.Lstat(rel)
+	if err != nil {
+		return nil, err
+	}
+	if !fi.Mode().IsRegular() {
+		return nil, fmt.Errorf("%s: %w", rel, ErrNotRegular)
+	}
+	return b.readOpenedMax(rel, max)
+}
+
+func (b *Brain) readOpenedMax(rel string, max int64) ([]byte, error) {
+	f, err := b.root.OpenFile(rel, os.O_RDONLY|syscall.O_NONBLOCK, 0)
+	if err != nil {
+		return nil, err
+	}
+	defer func() { _ = f.Close() }()
+	hfi, err := f.Stat()
+	if err != nil {
+		return nil, err
+	}
+	if !hfi.Mode().IsRegular() {
+		return nil, fmt.Errorf("%s: %w", rel, ErrNotRegular)
+	}
+	if max >= 0 && hfi.Size() > max {
+		return nil, fmt.Errorf("%s is %d bytes (limit %d): %w", rel, hfi.Size(), max, ErrTooLarge)
+	}
+	var r io.Reader = f
+	if wrapAfterStat != nil {
+		r = wrapAfterStat(r)
+	}
+	if max < 0 {
+		return io.ReadAll(r)
+	}
+	// The handle's size can grow after the check; bound the read itself.
+	data, err := io.ReadAll(io.LimitReader(r, max+1))
+	if err != nil {
+		return nil, err
+	}
+	if int64(len(data)) > max {
+		return nil, fmt.Errorf("%s grew past %d bytes while read: %w", rel, max, ErrTooLarge)
+	}
+	return data, nil
+}
+
+// wrapAfterStat is a test seam: it runs between the size check and the read,
+// and wraps the reader the read consumes. A package global: brainfs tests
+// must not use t.Parallel.
+var wrapAfterStat func(io.Reader) io.Reader
+
+// WalkRegular walks a brain-relative directory through the root and calls fn
+// for each regular file. Directories are descended; symlinks, FIFOs and
+// devices found by the walk are skipped. A walk root with any component that
+// is not a real directory goes to onErr as ErrNotRegular and nothing is
+// yielded. An entry error is passed to onErr and the walk continues; a nil
+// onErr ignores it.
+//
+// Accepted residual (hyperguild#157): a directory swapped for a symlink
+// between the listing and the read is followed. os.Root still keeps the read
+// inside the brain, but not inside relDir.
+func (b *Brain) WalkRegular(relDir string, fn func(rel string) error, onErr func(rel string, err error)) error {
+	relDir = filepath.ToSlash(relDir)
+	// fs.WalkDir stats its root with a follow, and os.Root allows a symlink
+	// that stays inside the brain: knowledge -> . would alias the whole
+	// brain. Require every component of the root to be a real directory
+	// (Lstat checks only the last one).
+	err := b.realDir(relDir)
+	if err != nil {
+		if onErr != nil {
+			onErr(relDir, err)
+		}
+		return nil
+	}
+	return fs.WalkDir(b.root.FS(), relDir, func(p string, d fs.DirEntry, err error) error {
+		if err != nil {
+			if onErr != nil {
+				onErr(p, err)
+			}
+			if d != nil && d.IsDir() {
+				return fs.SkipDir
+			}
+			return nil
+		}
+		if d.IsDir() || !d.Type().IsRegular() {
+			return nil
+		}
+		return fn(p)
+	})
+}

ingestion/internal/brainfs/brainfs_test.go

@@ -0,0 +1,191 @@
+package brainfs
+
+import (
+	"errors"
+	"io"
+	"io/fs"
+	"os"
+	"path/filepath"
+	"syscall"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// The handle check is what stops a FIFO swapped in after the Lstat. A FIFO
+// with no writer reads EOF at once, so a race test could not see the check
+// missing; here a writer holds the FIFO open, as any local process can, and
+// readOpened must refuse it promptly (PR #161 review).
+func TestReadOpenedRefusesAFIFOHeldOpenByAWriter(t *testing.T) {
+	dir := t.TempDir()
+	fifo := filepath.Join(dir, "p.md")
+	require.NoError(t, syscall.Mkfifo(fifo, 0o644))
+	w, err := os.OpenFile(fifo, os.O_RDWR, 0)
+	require.NoError(t, err)
+	defer func() { _ = w.Close() }()
+
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+
+	done := make(chan error, 1)
+	go func() { _, err := b.readOpened("p.md"); done <- err }()
+	select {
+	case err := <-done:
+		assert.True(t, errors.Is(err, ErrNotRegular), "got %v", err)
+	case <-time.After(2 * time.Second):
+		t.Fatal("readOpened blocked on a FIFO with a writer")
+	}
+}
+
+func TestReadRegularRefusesSymlinksAndReadsRegularFiles(t *testing.T) {
+	dir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "ok.md"), []byte("ok"), 0o644))
+	outside := filepath.Join(t.TempDir(), "s.md")
+	require.NoError(t, os.WriteFile(outside, []byte("secret"), 0o644))
+	require.NoError(t, os.Symlink(outside, filepath.Join(dir, "link.md")))
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+	got, err := b.ReadRegular("ok.md")
+	require.NoError(t, err)
+	assert.Equal(t, "ok", string(got))
+	_, err = b.ReadRegular("link.md")
+	assert.True(t, errors.Is(err, ErrNotRegular), "got %v", err)
+	_, err = b.ReadRegular("../" + filepath.Base(outside))
+	assert.Error(t, err)
+}
+
+func TestRelAcceptsPathsInsideAndRefusesEscapes(t *testing.T) {
+	dir := t.TempDir()
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+	for in, want := range map[string]string{
+		filepath.Join(dir, "wiki", "x.md"): "wiki/x.md",
+		filepath.Join(dir, "..foo", "x"):   "..foo/x",
+		dir:                                ".",
+	} {
+		got, err := b.Rel(in)
+		require.NoError(t, err, in)
+		assert.Equal(t, want, got, in)
+	}
+	for _, bad := range []string{filepath.Join(dir, "..", "x"), dir + "-evil/x", "/etc/passwd", filepath.Join(dir, "wiki", "..", "..", "x")} {
+		_, err := b.Rel(bad)
+		assert.Error(t, err, bad)
+	}
+}
+
+func TestWalkRegularYieldsOnlyRegularFiles(t *testing.T) {
+	dir := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(dir, "a"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "a", "n.md"), []byte("n"), 0o644))
+	require.NoError(t, os.Symlink(t.TempDir(), filepath.Join(dir, "a", "dirlink")))
+	require.NoError(t, os.Symlink(filepath.Join(dir, "a", "n.md"), filepath.Join(dir, "a", "filelink.md")))
+	require.NoError(t, syscall.Mkfifo(filepath.Join(dir, "a", "p.md"), 0o644))
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+	var got []string
+	require.NoError(t, b.WalkRegular(".", func(rel string) error { got = append(got, rel); return nil }, nil))
+	assert.Equal(t, []string{"a/n.md"}, got)
+}
+
+func TestReadRegularMaxRefusesAFileOverTheLimit(t *testing.T) {
+	dir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "big.md"), make([]byte, 100), 0o644))
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+	_, err = b.ReadRegularMax("big.md", 99)
+	assert.True(t, errors.Is(err, ErrTooLarge), "got %v", err)
+	got, err := b.ReadRegularMax("big.md", 100)
+	require.NoError(t, err)
+	assert.Len(t, got, 100)
+}
+
+func TestReadRegularMaxRefusesAndStopsReadingAFileThatGrowsPastTheLimit(t *testing.T) {
+	dir := t.TempDir()
+	p := filepath.Join(dir, "grow.md")
+	require.NoError(t, os.WriteFile(p, make([]byte, 10), 0o644))
+	consumed := &countingReader{}
+	wrapAfterStat = func(r io.Reader) io.Reader {
+		f, err := os.OpenFile(p, os.O_WRONLY|os.O_APPEND, 0)
+		require.NoError(t, err)
+		_, err = f.Write(make([]byte, 1000))
+		require.NoError(t, err)
+		require.NoError(t, f.Close())
+		consumed.r = r
+		return consumed
+	}
+	t.Cleanup(func() { wrapAfterStat = nil })
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+	got, err := b.ReadRegularMax("grow.md", 100)
+	assert.True(t, errors.Is(err, ErrTooLarge), "got %v", err)
+	assert.Nil(t, got)
+	assert.LessOrEqual(t, consumed.n, 101, "read past max+1 bytes")
+}
+
+type countingReader struct {
+	r io.Reader
+	n int
+}
+
+func (c *countingReader) Read(p []byte) (int, error) {
+	n, err := c.r.Read(p)
+	c.n += n
+	return n, err
+}
+
+func TestLstatDoesNotFollowSymlinksAndRefusesEscapes(t *testing.T) {
+	dir := t.TempDir()
+	outside := filepath.Join(t.TempDir(), "o.md")
+	require.NoError(t, os.WriteFile(outside, []byte("o"), 0o644))
+	require.NoError(t, os.Symlink(outside, filepath.Join(dir, "l.md")))
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+	fi, err := b.Lstat("l.md")
+	require.NoError(t, err)
+	assert.Equal(t, fs.ModeSymlink, fi.Mode().Type())
+	_, err = b.Lstat("../" + filepath.Base(filepath.Dir(outside)) + "/o.md")
+	assert.Error(t, err)
+}
+
+func TestWalkRegularReportsASymlinkedWalkRootAndYieldsNothing(t *testing.T) {
+	dir := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(dir, "real"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "real", "n.md"), []byte("n"), 0o644))
+	require.NoError(t, os.Symlink("real", filepath.Join(dir, "alias")))
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+	var got []string
+	var errs []error
+	require.NoError(t, b.WalkRegular("alias", func(rel string) error { got = append(got, rel); return nil },
+		func(_ string, err error) { errs = append(errs, err) }))
+	assert.Empty(t, got)
+	require.Len(t, errs, 1)
+	assert.ErrorIs(t, errs[0], ErrNotRegular)
+}
+
+func TestWalkRegularReportsASymlinkedIntermediateComponentOfTheWalkRoot(t *testing.T) {
+	dir := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(dir, "real", "sub"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "real", "sub", "n.md"), []byte("n"), 0o644))
+	require.NoError(t, os.Symlink("real", filepath.Join(dir, "alias")))
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+	var got []string
+	var errs []error
+	require.NoError(t, b.WalkRegular("alias/sub", func(rel string) error { got = append(got, rel); return nil },
+		func(_ string, err error) { errs = append(errs, err) }))
+	assert.Empty(t, got)
+	require.Len(t, errs, 1)
+	assert.ErrorIs(t, errs[0], ErrNotRegular)
+}

ingestion/internal/brainfs/brainfstest/brainfstest.go

@@ -0,0 +1,103 @@
+// Package brainfstest is the shared harness for hyperguild#157's swap-race
+// tests: it keeps swapping a regular note, a symlink to an outside file, or a
+// FIFO (with a writer held open) into a path while a reader under test loops.
+// It observes two things: no sentinel byte from the outside file reaches the
+// reader's output, and the reader returns within a timeout. It does not cover
+// hard links, other paths into the reader, or races it does not generate.
+package brainfstest
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+	"sync"
+	"sync/atomic"
+	"syscall"
+	"testing"
+	"time"
+)
+
+// Sentinel marks the outside file's contents.
+const Sentinel = "zqbrainfssentinelonefiftyseven"
+
+// Outside writes a file outside any brain dir containing Sentinel.
+func Outside(t *testing.T) string {
+	t.Helper()
+	p := filepath.Join(t.TempDir(), "secret.md")
+	if err := os.WriteFile(p, []byte("# secret\n\n"+Sentinel), 0o644); err != nil {
+		t.Fatal(err)
+	}
+	return p
+}
+
+// StartSwap renames, in a loop, a regular note (content inside) and either
+// a symlink to outside or a FIFO into path, until the test ends. FIFOs get a
+// writer held open until the swapper exits, so a reader that skips the
+// handle check parks forever instead of reading EOF. The swapper is stopped
+// and awaited before t.TempDir cleanup.
+func StartSwap(t *testing.T, path, inside, outside string, fifo bool) {
+	t.Helper()
+	var stop atomic.Bool
+	var wg sync.WaitGroup
+	wg.Add(1)
+	go func() {
+		defer wg.Done()
+		tmp := path + ".swap"
+		var writers []*os.File
+		defer func() {
+			for _, w := range writers {
+				_ = w.Close()
+			}
+		}()
+		for i := 0; !stop.Load(); i++ {
+			_ = os.Remove(tmp)
+			switch {
+			case i%2 == 0:
+				_ = os.WriteFile(tmp, []byte(inside), 0o644)
+			case fifo:
+				if err := syscall.Mkfifo(tmp, 0o644); err == nil {
+					if w, err := os.OpenFile(tmp, os.O_RDWR, 0); err == nil {
+						writers = append(writers, w)
+					}
+				}
+			default:
+				_ = os.Symlink(outside, tmp)
+			}
+			_ = os.Rename(tmp, path)
+		}
+	}()
+	t.Cleanup(func() { stop.Store(true); wg.Wait() })
+}
+
+// AssertNoLeak loops read for d while a symlink swapper runs on path, and
+// fails if any output contains Sentinel.
+func AssertNoLeak(t *testing.T, path, inside string, d time.Duration, read func() string) {
+	t.Helper()
+	StartSwap(t, path, inside, Outside(t), false)
+	leaks, iters := 0, 0
+	for deadline := time.Now().Add(d); time.Now().Before(deadline); iters++ {
+		leaks += strings.Count(read(), Sentinel)
+	}
+	if leaks > 0 {
+		t.Fatalf("outside file leaked %d times in %d iterations", leaks, iters)
+	}
+}
+
+// AssertNoHang loops read for d while a FIFO swapper (held writers) runs on
+// path, and fails if a read does not return within timeout.
+func AssertNoHang(t *testing.T, path, inside string, d, timeout time.Duration, read func()) {
+	t.Helper()
+	StartSwap(t, path, inside, Outside(t), true)
+	done := make(chan struct{})
+	go func() {
+		for deadline := time.Now().Add(d); time.Now().Before(deadline); {
+			read()
+		}
+		close(done)
+	}()
+	select {
+	case <-done:
+	case <-time.After(timeout):
+		t.Fatal("reader hung on a swapped-in FIFO with a writer held open")
+	}
+}

ingestion/internal/mcp/readexcerpt_root_test.go

@@ -0,0 +1,34 @@
+package mcp
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs/brainfstest"
+)
+
+// hyperguild#157 slice 2: readExcerpt (brain_context) read by path, so a
+// symlink in the Syncthing-shared brain put an outside file in context, and
+// a FIFO hung it. It now reads through brainfs.
+func TestReadExcerptRefusesSymlinksAndSurvivesSwapRaces(t *testing.T) {
+	brain := t.TempDir()
+	facts := filepath.Join(brain, "wiki", "w", "facts")
+	require.NoError(t, os.MkdirAll(facts, 0o755))
+	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(facts, "leak.md")))
+	assert.NotContains(t, readExcerpt(brain, "wiki/w/facts/leak.md", 500), brainfstest.Sentinel)
+
+	p := filepath.Join(facts, "r.md")
+	require.NoError(t, os.WriteFile(p, []byte("---\nx: y\n---\ninside"), 0o644))
+	assert.Equal(t, "inside", readExcerpt(brain, "wiki/w/facts/r.md", 500))
+	brainfstest.AssertNoLeak(t, p, "---\nx: y\n---\ninside", 1500*time.Millisecond, func() string {
+		return readExcerpt(brain, "wiki/w/facts/r.md", 500)
+	})
+	brainfstest.AssertNoHang(t, p, "---\nx: y\n---\ninside", 1500*time.Millisecond, 6*time.Second, func() {
+		_ = readExcerpt(brain, "wiki/w/facts/r.md", 500)
+	})
+}

ingestion/internal/mcp/tools_context.go

@@ -4,7 +4,7 @@ import (
 	"context"
 	"encoding/json"
 	"fmt"
-	"os"
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 	"path/filepath"
 	"sort"
 	"strings"
@@ -181,8 +181,13 @@ func readExcerpt(brainDir, relPath string, maxLen int) string {
 	if relPath == "" {
 		return ""
 	}
-	full := filepath.Join(brainDir, filepath.FromSlash(relPath))
+	// Through the brain root, regular files only (hyperguild#157).
-	content, err := os.ReadFile(full)
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return ""
+	}
+	defer func() { _ = bfs.Close() }()
+	content, err := bfs.ReadRegular(filepath.ToSlash(relPath))
 	if err != nil {
 		return ""
 	}

ingestion/internal/notes/edit.go

@@ -5,6 +5,7 @@ import (
 	"encoding/hex"
 	"errors"
 	"fmt"
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 	"os"
 	"path/filepath"
 	"strings"
@@ -71,14 +72,18 @@ func ReadScoped(brainDir, path string, scope Scope) ([]byte, error) {
 }
 
 func readContained(t Target) ([]byte, error) {
-	fi, err := os.Stat(t.Abs)
+	// Through the brain root, regular files only, size checked on the opened
+	// handle (hyperguild#157): Resolve's Lstat could be raced by a swap, and
+	// os.ReadFile blocked on a FIFO.
+	bfs, err := brainfs.Open(t.Brain)
 	if err != nil {
-		return nil, fmt.Errorf("notes: stat %s: %w", t.Rel, err)
+		return nil, fmt.Errorf("notes: %w", err)
 	}
-	if fi.Size() > maxNoteBytes {
+	defer func() { _ = bfs.Close() }()
-		return nil, fmt.Errorf("%w: %s is %d bytes (limit %d)", ErrTooLarge, t.Rel, fi.Size(), maxNoteBytes)
+	b, err := bfs.ReadRegularMax(t.Rel, maxNoteBytes)
+	if errors.Is(err, brainfs.ErrTooLarge) {
+		return nil, fmt.Errorf("%w: %s (limit %d)", ErrTooLarge, t.Rel, maxNoteBytes)
 	}
-	b, err := os.ReadFile(t.Abs)
 	if err != nil {
 		return nil, fmt.Errorf("notes: read %s: %w", t.Rel, err)
 	}

ingestion/internal/notes/path.go

@@ -60,6 +60,7 @@ var (
 type Target struct {
 	Rel   string // brain-relative, cleaned
 	Abs   string // absolute, symlink-checked
+	Brain string // the brain root Rel is relative to
 }
 
 // Resolve canonicalises path, then checks it against the scope's allowlist,
@@ -109,7 +110,7 @@ func Resolve(brainDir, path string, scope Scope) (Target, error) {
 		return Target{}, err
 	}
 
-	return Target{Rel: clean, Abs: abs}, nil
+	return Target{Rel: clean, Abs: abs, Brain: brainDir}, nil
 }
 
 // allow enforces the scope's allowlist. The two scopes are DISJOINT, not

ingestion/internal/notes/read_root_test.go

@@ -0,0 +1,40 @@
+package notes
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs/brainfstest"
+)
+
+// hyperguild#157 slice 2: ReadScoped (brain_read) Lstat-checked the final
+// component, then reopened by name with os.ReadFile: a swap after the check
+// was followed, and a FIFO blocked the read. It now reads through brainfs.
+func TestReadScopedRefusesSymlinksAndSurvivesSwapRaces(t *testing.T) {
+	brain := t.TempDir()
+	facts := filepath.Join(brain, "wiki", "w", "facts")
+	require.NoError(t, os.MkdirAll(facts, 0o755))
+	p := filepath.Join(facts, "r.md")
+	read := func() string {
+		b, _ := ReadScoped(brain, "wiki/w/facts/r.md", ScopeNotes)
+		return string(b)
+	}
+	require.NoError(t, os.WriteFile(p, []byte("inside"), 0o644))
+	assert.Equal(t, "inside", read())
+	brainfstest.AssertNoLeak(t, p, "inside", 1500*time.Millisecond, read)
+	brainfstest.AssertNoHang(t, p, "inside", 1500*time.Millisecond, 6*time.Second, func() { _ = read() })
+}
+
+func TestReadScopedRefusesANoteOverMaxNoteBytes(t *testing.T) {
+	brain := t.TempDir()
+	facts := filepath.Join(brain, "wiki", "w", "facts")
+	require.NoError(t, os.MkdirAll(facts, 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(facts, "big.md"), make([]byte, maxNoteBytes+1), 0o644))
+	_, err := ReadScoped(brain, "wiki/w/facts/big.md", ScopeNotes)
+	assert.ErrorIs(t, err, ErrTooLarge)
+}

ingestion/internal/search/brainroot_test.go

@@ -0,0 +1,174 @@
+package search
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+	"sync"
+	"sync/atomic"
+	"syscall"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// hyperguild#157 option 1: search walked and read the brain by path, so a
+// symlink anywhere in the Syncthing-shared brain dir (wiki/<w>/<h>/leak.md ->
+// /any/file) put the target's contents in brain_query results (reproduced in
+// the PR #156 review). Search now walks and reads through an os.Root on the
+// brain dir and only reads regular files.
+
+const sentinel157 = "zqsentinelonefiftyseven"
+
+func searchBrain(t *testing.T) (brain, facts, outside string) {
+	t.Helper()
+	brain = t.TempDir()
+	facts = filepath.Join(brain, "wiki", "w", "facts")
+	require.NoError(t, os.MkdirAll(facts, 0o755))
+	require.NoError(t, os.MkdirAll(filepath.Join(brain, "knowledge"), 0o755))
+	outside = filepath.Join(t.TempDir(), "secret.md")
+	require.NoError(t, os.WriteFile(outside, []byte("# secret\n\n"+sentinel157), 0o644))
+	return brain, facts, outside
+}
+
+func leaked(rs []Result) int {
+	n := 0
+	for _, r := range rs {
+		n += strings.Count(r.Excerpt+r.Title, sentinel157)
+	}
+	return n
+}
+
+func TestQueryDoesNotFollowASymlinkInTheWiki(t *testing.T) {
+	brain, facts, outside := searchBrain(t)
+	require.NoError(t, os.Symlink(outside, filepath.Join(facts, "leak.md")))
+	require.NoError(t, os.WriteFile(filepath.Join(facts, "real.md"), []byte("# real\n\nzqrealnote"), 0o644))
+	rs, err := Query(brain, QueryOptions{Query: sentinel157, Limit: 10})
+	require.NoError(t, err)
+	assert.Zero(t, leaked(rs))
+	rs, err = Query(brain, QueryOptions{Query: "zqrealnote", Limit: 10})
+	require.NoError(t, err)
+	assert.Len(t, rs, 1, "regular notes are still found")
+}
+
+func TestQueryDoesNotFollowASymlinkedDirectory(t *testing.T) {
+	brain, _, outside := searchBrain(t)
+	require.NoError(t, os.Symlink(filepath.Dir(outside), filepath.Join(brain, "wiki", "linked")))
+	rs, err := Query(brain, QueryOptions{Query: sentinel157, Limit: 10})
+	require.NoError(t, err)
+	assert.Zero(t, leaked(rs))
+}
+
+// A search root that is a symlink staying inside the brain (wiki/<w> -> ..)
+// was followed by fs.WalkDir, aliasing raw/ and root files into results
+// (PR #166 review). The root is now Lstat-checked and skipped.
+func TestQueryDoesNotFollowASymlinkedWingRootInsideTheBrain(t *testing.T) {
+	brain, _, _ := searchBrain(t)
+	require.NoError(t, os.MkdirAll(filepath.Join(brain, "raw"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "raw", "r.md"), []byte("# r\n\nzqrawonly"), 0o644))
+	require.NoError(t, os.Symlink("..", filepath.Join(brain, "wiki", "alias")))
+	rs, err := Query(brain, QueryOptions{Query: "zqrawonly", Wing: "alias", Limit: 10})
+	require.NoError(t, err)
+	assert.Empty(t, rs)
+}
+
+// With a hall the search root is wiki/<wing>/<hall>; a symlinked <wing> with
+// a real <hall> directory under its target was followed (PR #166 round 2).
+func TestQueryDoesNotFollowASymlinkedWingUnderAWingAndHallRoot(t *testing.T) {
+	brain, _, _ := searchBrain(t)
+	require.NoError(t, os.MkdirAll(filepath.Join(brain, "raw", "facts"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "raw", "facts", "r.md"), []byte("# r\n\nzqrawhall"), 0o644))
+	require.NoError(t, os.Symlink(filepath.Join("..", "raw"), filepath.Join(brain, "wiki", "alias")))
+	rs, err := Query(brain, QueryOptions{Query: "zqrawhall", Wing: "alias", Hall: "facts", Limit: 10})
+	require.NoError(t, err)
+	assert.Empty(t, rs)
+}
+
+// swapInto keeps renaming a regular note, and either a symlink to outside or
+// a FIFO, into path. Each FIFO has a writer held open (as any local process
+// can): a FIFO with no writer reads EOF at once, which would let a reader
+// that skips the handle check pass (PR #161 round 2: with a held writer, a
+// bypass of readOpened hung Query after 5 iterations).
+// startSwap runs swapInto until the test ends and waits for it before
+// t.TempDir's cleanup (hyperguild#162).
+func startSwap(t *testing.T, path, outside string, fifo bool) {
+	t.Helper()
+	var stop atomic.Bool
+	var wg sync.WaitGroup
+	wg.Add(1)
+	go func() { defer wg.Done(); swapInto(path, outside, fifo, &stop) }()
+	t.Cleanup(func() { stop.Store(true); wg.Wait() })
+}
+
+func swapInto(path, outside string, fifo bool, stop *atomic.Bool) {
+	tmp := path + ".swap"
+	// Writers stay open until the swapper exits, so a reader parked on a
+	// FIFO stays parked (closing one would hand the reader EOF and hide the
+	// hang). Past the fd limit, new FIFOs simply have no writer.
+	var writers []*os.File
+	defer func() {
+		for _, w := range writers {
+			_ = w.Close()
+		}
+	}()
+	for i := 0; !stop.Load(); i++ {
+		_ = os.Remove(tmp)
+		switch {
+		case i%2 == 0:
+			_ = os.WriteFile(tmp, []byte("# r\n\nzqinside "+"zqracenote"), 0o644)
+		case fifo:
+			if err := syscall.Mkfifo(tmp, 0o644); err == nil {
+				if w, err := os.OpenFile(tmp, os.O_RDWR, 0); err == nil {
+					writers = append(writers, w)
+				}
+			}
+		default:
+			_ = os.Symlink(outside, tmp)
+		}
+		_ = os.Rename(tmp, path)
+	}
+}
+
+func TestQueryLeaksNothingUnderASymlinkSwapRace(t *testing.T) {
+	brain, facts, outside := searchBrain(t)
+	startSwap(t, filepath.Join(facts, "r.md"), outside, false)
+	leaks, iters := 0, 0
+	for deadline := time.Now().Add(1500 * time.Millisecond); time.Now().Before(deadline); iters++ {
+		rs, _ := Query(brain, QueryOptions{Query: sentinel157, Limit: 10})
+		leaks += leaked(rs)
+	}
+	if leaks > 0 {
+		t.Fatalf("outside file leaked %d times in %d iterations", leaks, iters)
+	}
+}
+
+func TestQueryDoesNotHangUnderAFIFOSwapRace(t *testing.T) {
+	brain, facts, outside := searchBrain(t)
+	startSwap(t, filepath.Join(facts, "r.md"), outside, true)
+	done := make(chan struct{})
+	go func() {
+		for deadline := time.Now().Add(1500 * time.Millisecond); time.Now().Before(deadline); {
+			_, _ = Query(brain, QueryOptions{Query: "zqracenote", Limit: 10})
+		}
+		close(done)
+	}()
+	select {
+	case <-done:
+	case <-time.After(6 * time.Second):
+		if f, err := os.OpenFile(filepath.Join(facts, "r.md"), os.O_WRONLY|syscall.O_NONBLOCK, 0); err == nil {
+			_ = f.Close()
+		}
+		t.Fatal("search hung on a swapped-in FIFO")
+	}
+}
+
+// hydrate (vector-only hits) reads by relative path; it must refuse a symlink.
+func TestHydrateRefusesASymlink(t *testing.T) {
+	brain, facts, outside := searchBrain(t)
+	require.NoError(t, os.Symlink(outside, filepath.Join(facts, "leak.md")))
+	r, err := hydrate(brain, "wiki/w/facts/leak.md")
+	assert.Error(t, err)
+	assert.NotContains(t, r.Excerpt, sentinel157)
+}

ingestion/internal/search/search.go

@@ -5,6 +5,7 @@ import (
 	"bufio"
 	"context"
 	"fmt"
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 	sharedfm "github.com/mathiasbq/hyperguild/ingestion/internal/frontmatter"
 	"log/slog"
 	"os"
@@ -119,20 +120,30 @@ func QueryContext(ctx context.Context, brainDir string, opts QueryOptions) ([]Re
 		return nil, err
 	}
 
+	// Walk and read through an os.Root on the brain dir, regular files only
+	// (hyperguild#157): a symlink planted in the Syncthing-shared brain must
+	// not put an outside file in results, nor a FIFO hang the query.
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return nil, fmt.Errorf("search: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
+
 	var results []Result
 	for _, dir := range roots {
 		if _, statErr := os.Stat(dir); os.IsNotExist(statErr) {
 			continue
 		}
-		err := filepath.WalkDir(dir, func(path string, d os.DirEntry, err error) error {
+		relDir, relErr := bfs.Rel(dir)
-			if err != nil {
+		if relErr != nil {
-				slog.Warn("search: skipping path", "path", path, "err", err)
+			return nil, fmt.Errorf("search: %w", relErr)
+		}
+		err := bfs.WalkRegular(relDir, func(relPath string) error {
+			if !strings.HasSuffix(relPath, ".md") {
 				return nil
 			}
-			if d.IsDir() || !strings.HasSuffix(path, ".md") {
+			path := filepath.Join(brainDir, filepath.FromSlash(relPath))
-				return nil
+			content, err := bfs.ReadRegular(relPath)
-			}
-			content, err := os.ReadFile(path)
 			if err != nil {
 				slog.Warn("search: skipping unreadable file", "path", path, "err", err)
 				return nil
@@ -155,7 +166,7 @@ func QueryContext(ctx context.Context, brainDir string, opts QueryOptions) ([]Re
 			origin, writtenBy := extractProvenance(string(content))
 			results = append(results, Result{
 				Path:    rel,
-				Title:   extractTitle(string(content), d.Name()),
+				Title:   extractTitle(string(content), filepath.Base(relPath)),
 				Excerpt: excerpt(string(content), 300),
 				Score:   score,
 				Wing:    wing,
@@ -166,6 +177,8 @@ func QueryContext(ctx context.Context, brainDir string, opts QueryOptions) ([]Re
 				WrittenBy: writtenBy,
 			})
 			return nil
+		}, func(p string, err error) {
+			slog.Warn("search: skipping path", "path", p, "err", err)
 		})
 		if err != nil {
 			return nil, err
@@ -275,8 +288,13 @@ func pathInScope(relPath, wing, hall string) bool {
 // excerpt, wing, and hall populated. Used for paths that surface only
 // via vector search.
 func hydrate(brainDir, relPath string) (Result, error) {
-	full := filepath.Join(brainDir, filepath.FromSlash(relPath))
+	// Through the brain root, regular files only (hyperguild#157).
-	content, err := os.ReadFile(full)
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return Result{}, err
+	}
+	defer func() { _ = bfs.Close() }()
+	content, err := bfs.ReadRegular(filepath.ToSlash(relPath))
 	if err != nil {
 		return Result{}, err
 	}

ingestion/internal/vectorstore/sync.go

@@ -2,12 +2,15 @@ package vectorstore
 
 import (
 	"context"
+	"errors"
 	"fmt"
+	"io/fs"
 	"log/slog"
-	"os"
+	"path"
-	"path/filepath"
 	"strings"
 	"time"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 )
 
 // Embedder produces dense vectors. The embed package's Client satisfies
@@ -90,31 +93,38 @@ func Sync(ctx context.Context, brainDir string, store Store, embedder Embedder)
 	}
 	seenParents := make(map[string]struct{})
 
+	// Through the brain root, regular files only (hyperguild#157): the brain
+	// is a Syncthing folder, and os.ReadFile followed a synced symlink into
+	// the embeddings and blocked on a FIFO.
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return res, fmt.Errorf("open brain: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
+
 	for _, sub := range scanDirs {
-		root := filepath.Join(brainDir, sub)
+		if _, err := bfs.Lstat(sub); errors.Is(err, fs.ErrNotExist) {
-		if _, err := os.Stat(root); os.IsNotExist(err) {
 			continue
 		}
-
+		// Any other walk error, including a scan root that is a symlink,
-		err = filepath.WalkDir(root, func(path string, d os.DirEntry, err error) error {
+		// aborts the run below.
-			if err != nil {
+		var walkErr error
-				return err
+		onErr := func(rel string, err error) {
+			if walkErr == nil {
+				walkErr = fmt.Errorf("%s: %w", rel, err)
 			}
-			if d.IsDir() || !strings.HasSuffix(path, ".md") || d.Name() == "_index.md" {
+		}
+		err = bfs.WalkRegular(sub, func(relSlash string) error {
+			if !strings.HasSuffix(relSlash, ".md") || path.Base(relSlash) == "_index.md" {
 				return nil
 			}
-			rel, err := filepath.Rel(brainDir, path)
-			if err != nil {
-				return err
-			}
-			relSlash := filepath.ToSlash(rel)
 			seenParents[relSlash] = struct{}{}
 
 			if ps, ok := parents[relSlash]; ok {
 				// File already has chunks in the store. Re-embed only when
 				// the file has been edited since the oldest chunk was
 				// written. Tolerate clock skew with a sub-second grace.
-				info, statErr := d.Info()
+				info, statErr := bfs.Lstat(relSlash)
 				if statErr != nil {
 					res.Errors = append(res.Errors, fmt.Errorf("stat %s: %w", relSlash, statErr))
 					return nil
@@ -132,7 +142,7 @@ func Sync(ctx context.Context, brainDir string, store Store, embedder Embedder)
 				}
 			}
 
-			content, readErr := os.ReadFile(path)
+			content, readErr := bfs.ReadRegular(relSlash)
 			if readErr != nil {
 				res.Errors = append(res.Errors, fmt.Errorf("read %s: %w", relSlash, readErr))
 				return nil
@@ -151,7 +161,12 @@ func Sync(ctx context.Context, brainDir string, store Store, embedder Embedder)
 				res.Added++
 			}
 			return nil
-		})
+		}, onErr)
+		if err == nil {
+			err = walkErr
+		}
+		// Abort before the delete pass: an incomplete walk would leave
+		// seenParents short and delete chunks of files that still exist.
 		if err != nil {
 			return res, fmt.Errorf("walk %s: %w", sub, err)
 		}

ingestion/internal/vectorstore/sync_root_test.go

@@ -0,0 +1,126 @@
+package vectorstore_test
+
+import (
+	"context"
+	"os"
+	"path/filepath"
+	"strings"
+	"sync"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs/brainfstest"
+	"github.com/mathiasbq/hyperguild/ingestion/internal/vectorstore"
+)
+
+// recordingEmbedder keeps every text it was asked to embed.
+type recordingEmbedder struct {
+	mu    sync.Mutex
+	texts []string
+}
+
+func (e *recordingEmbedder) Embed(_ context.Context, text string) ([]float32, error) {
+	e.mu.Lock()
+	defer e.mu.Unlock()
+	e.texts = append(e.texts, text)
+	return []float32{1}, nil
+}
+
+func (e *recordingEmbedder) all() string {
+	e.mu.Lock()
+	defer e.mu.Unlock()
+	return strings.Join(e.texts, "\n")
+}
+
+// hyperguild#157 slice 3: Sync walked wiki/ and knowledge/ and read each .md
+// with os.ReadFile, so a symlinked note had its target embedded and served by
+// semantic search, and a FIFO stalled the sync.
+func TestSyncRefusesSymlinkedNotesAndSurvivesSwapRaces(t *testing.T) {
+	brain := t.TempDir()
+	writeNote(t, brain, "wiki/w/facts/ok.md", "inside note")
+	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(brain, "wiki", "w", "facts", "leak.md")))
+
+	emb := &recordingEmbedder{}
+	store := &stubStore{}
+	_, err := vectorstore.Sync(context.Background(), brain, store, emb)
+	require.NoError(t, err)
+	assert.Contains(t, emb.all(), "inside note", "positive control: the regular note is embedded")
+	assert.NotContains(t, emb.all(), brainfstest.Sentinel)
+	for p := range store.upserts {
+		assert.NotContains(t, p, "leak.md")
+	}
+
+	p := filepath.Join(brain, "knowledge", "r.md")
+	require.NoError(t, os.MkdirAll(filepath.Dir(p), 0o755))
+	sync := func() string {
+		e := &recordingEmbedder{}
+		_, _ = vectorstore.Sync(context.Background(), brain, &stubStore{}, e)
+		return e.all()
+	}
+	brainfstest.AssertNoLeak(t, p, "inside", 1500*time.Millisecond, sync)
+	brainfstest.AssertNoHang(t, p, "inside", 1500*time.Millisecond, 6*time.Second, func() { _ = sync() })
+}
+
+// Chunks embedded from a symlinked note before this fix are deleted: the
+// note is no longer seen, so the delete pass drops its rows.
+func TestSyncDeletesChunksOfASymlinkedNote(t *testing.T) {
+	brain := t.TempDir()
+	writeNote(t, brain, "wiki/w/facts/ok.md", "inside note")
+	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(brain, "wiki", "w", "facts", "leak.md")))
+	store := &stubStore{known: map[string]time.Time{
+		"wiki/w/facts/leak.md#0001": {},
+		"wiki/w/facts/ok.md#0001":   {},
+	}}
+	_, err := vectorstore.Sync(context.Background(), brain, store, &recordingEmbedder{})
+	require.NoError(t, err)
+	assert.Equal(t, []string{"wiki/w/facts/leak.md#0001"}, store.deletes)
+}
+
+// A walk error aborts Sync before the delete pass, so chunks of files the
+// walk could not see are kept.
+func TestSyncAbortsBeforeDeletingWhenASubdirIsUnreadable(t *testing.T) {
+	if os.Geteuid() == 0 {
+		t.Skip("root ignores directory permissions")
+	}
+	brain := t.TempDir()
+	writeNote(t, brain, "wiki/w/facts/ok.md", "inside note")
+	locked := filepath.Join(brain, "wiki", "w")
+	require.NoError(t, os.Chmod(locked, 0o000))
+	t.Cleanup(func() { _ = os.Chmod(locked, 0o755) })
+	store := &stubStore{known: map[string]time.Time{"wiki/w/facts/ok.md#0001": {}}}
+	_, err := vectorstore.Sync(context.Background(), brain, store, &recordingEmbedder{})
+	assert.Error(t, err)
+	assert.Empty(t, store.deletes)
+}
+
+// A scan root that is a symlink inside the brain (knowledge -> .) was
+// followed by fs.WalkDir, aliasing raw/, sessions/ and root files into the
+// index. Sync now aborts on it, before embedding or deleting anything.
+func TestSyncAbortsOnASymlinkedScanRoot(t *testing.T) {
+	brain := t.TempDir()
+	writeNote(t, brain, "wiki/w/a.md", "wiki note")
+	writeNote(t, brain, "sessions/s1.md", "session note")
+	require.NoError(t, os.Symlink(".", filepath.Join(brain, "knowledge")))
+	emb := &recordingEmbedder{}
+	store := &stubStore{known: map[string]time.Time{"wiki/w/a.md#0001": {}}}
+	_, err := vectorstore.Sync(context.Background(), brain, store, emb)
+	assert.Error(t, err)
+	assert.NotContains(t, emb.all(), "session note")
+	for p := range store.upserts {
+		assert.False(t, strings.HasPrefix(p, "knowledge/"), "upserted %s", p)
+	}
+	assert.Empty(t, store.deletes)
+}
+
+// A missing scan root is skipped; the other root still syncs.
+func TestSyncSkipsAMissingScanRoot(t *testing.T) {
+	brain := t.TempDir()
+	writeNote(t, brain, "wiki/w/a.md", "wiki note")
+	emb := &recordingEmbedder{}
+	_, err := vectorstore.Sync(context.Background(), brain, &stubStore{}, emb)
+	require.NoError(t, err)
+	assert.Contains(t, emb.all(), "wiki note")
+}